Crystal structure of Thr132Ala of ST1022 from Sulfolobus tokodaii

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.242 

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Crystal structure of glutamine receptor protein from Sulfolobus tokodaii strain 7 in complex with its effector L-glutamine: implications of effector binding in molecular association and DNA binding

Kumarevel, T.S.Nakano, N.Ponnuraj, K.Gopinath, S.C.B.Sakamoto, K.Shinkai, A.Kumar, P.K.R.Yokoyama, S.

(2008) Nucleic Acids Res 36: 4808-4820

  • DOI: https://doi.org/10.1093/nar/gkn456
  • Primary Citation of Related Structures:  
    2E7W, 2E7X, 2EFN, 2EFO, 2EFP, 2EFQ, 2PMH, 2PN6, 2YX4, 2YX7

  • PubMed Abstract: 

    Genome analyses have revealed that members of the Lrp/AsnC family of transcriptional regulators are widely distributed among prokaryotes, including both bacteria and archaea. These regulatory proteins are involved in cellular metabolism in both global and specific manners, depending on the availability of the exogenous amino acid effectors. Here we report the first crystal structure of glutamine receptor protein (Grp) from Sulfolobus tokodaii strain 7, in the ligand-free and glutamine-bound (Grp-Gln) forms. Although the overall structures of both molecules are similar, a significant conformational change was observed at the ligand [L-glutamine (Gln)] binding site in the effector domain, which may be essential for further stabilization of the octameric structure, and in turn for facilitating DNA binding. In addition, we predicted promoter for the grp gene, and these analyses suggested the importance of cooperative binding to the protein. To gain insights into the ligand-induced conformational changes, we mutated all of the ligand-binding residues in Grp, and revealed the importance of Gln binding by biochemical and structural analyses. Further structural analyses showed that Y77 is crucial for ligand binding, and that the residues T132 and T134, which are highly conserved among the Lrp family of proteins, fluctuates between the active and inactive conformations, thus affecting protein oligomerization for DNA binding.

  • Organizational Affiliation

    RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan. tskvel@spring8.or.jp

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
150aa long hypothetical transcriptional regulator150Sulfurisphaera tokodaii str. 7Mutation(s): 1 
Gene Names: ST1022
Find proteins for F9VNT4 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7))
Explore F9VNT4 
Go to UniProtKB:  F9VNT4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF9VNT4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.242 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.697α = 90
b = 103.697β = 90
c = 74.939γ = 90
Software Package:
Software NamePurpose
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.2: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-10-25
    Changes: Data collection, Refinement description